The availability of large volumes of genomic data, including complete genome sequences, as resulted in the need for biologists to adopt new research paradigms to use these data effectively in the context of a particular biological research question. Increasingly, the scientific community is turning to powerful computational and statistical methods for generating hypotheses about putative candidate genes and their functions that can subsequently be tested in the laboratory. Although many researchers see clearly the need to adopt computational methods in their research programs, the transition can be difficult due to a lack of specialized training programs and "off the shelf" bioinformatics software solutions. If the promise of the human genome project is to be realized, it is critical that laboratory scientists not become disenfranchised by genomic data but rather are empowered to use the information to drive knowledge discovery. To help biologists lay the foundation for using bioinformatics tools and resources in their research programs, we propose a 7-8 day short course called "Genome Sequence Analysis: Theory and Practice" to be offered each year for 5 years beginning in late May or early June of 2002. Our overall goal for the genome sequence analysis short course is to convey a deeper understanding of the computational tools that can be brought to bear on evaluating and interpreting genomic sequence data as well as to address practical issues of how to organize and manage the results of these analyses. The "Genuine Sequence Analysis: Theory and Practice" course will cover both the process of analyzing genomic sequences to identify biologically significant features as well as computational approaches for the prediction of function for genes and gene products. It will bring scientists with training in computational biology, mathematics, and computer science together with wet bench biologists who are seeking to integrate bioinformatics methods into their research, Participants will be introduced to the mathematical theory behind many of the commonly used computational tools for sequence analysis and to the implementation of these algorithms as analysis tools for genomic sequence data. To illustrate the integration of bioinformatics with wet-bench biology, the course will include research seminars by biologists who are currently using bioinformatics tools in conjunction with a variety of methods for experimental verification of computationally-based hypotheses.